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James Sacco | Curriculum Vitae
Bioinformatics Scientist
Department of Gene and Cell Therapy
ASC Therapeutics
Milpitas, CA, 95035
Independent, self-motivated bioinformatics scientist, with five years of experience in cancer immunotherapy and gene therapy for rare diseases. Specialist in computational biology of CRISPR gene editing. An analytical thinker and quick learner, with experience in next-generation sequencing (NGS) methods, such as RNA-Seq, and pipeline development. Integrated genotype phenotype data to predict disease severity. Developed machine learning applications to analyze population-scale genomic and real-world patient data. Experienced with cross-functional teams of diverse cultural and technical backgrounds.
Employment
Bioinformatics Scientist
ASC Therapeutics
Milpitas, CA
Present - 2021
● Quantify and characterize CRISPR gene modifications, with both custom and open-source tools for genomic data analysis.
● Query, retrieve, and integrate data from public genomics databases, to enhance on-target gene editing with sequence alignment protocols.
● Examine concordance and sensitivity of five open-source CRISPR off-target detection methods (CALITAS, CHANGE-Seq, CRISPResso, GUIDE-Seq, and Cas-OFFinder).
● Streamline high-performace analyses for bench scientists by constructing custom data pipelines.
● Spearhead implementation of version control, and programming best practices.
Biomarker Data Analyst II
Genentech (Contract)
South San Francisco, CA
2020 - 2019
● Established department-first machine learning pipeline to study effects of biomarker operations on quality of cancer immunotherapy assays.
● Upgraded data operations for six data streams, including flow cytometry, biomarker operations, and oncology data warehouses.
● Monitored and solved sample data quality issues for two cancer immunotherapy trial arms.
Data Curator
Genentech (Contract)
South San Francisco, CA
2019 - 2018
● Collaborated with AI engineers to create an ETL pipeline for multi-modal survival prediction and patient stratification, by using Python machine learning and R/Bioconductor to integrate gene panel and RNA-Seq data.
● Designed ETL data pipeline for integration of real-world EHRs into deep learning module, using Python, SQL, and Apache Spark.
● Organized and managed close coordination of gRED Artificial Intelligence, data management, and DevOps functions, to bring clinical machine learning from prototype to production.
PROGRAMMING SKILLS
R
Python
Linux
Git
GitHub
Markdown
LANGUAGES
English: Native
Spanish: Native
Data Curator, Bioinformatics Analyst
BioMarin Pharmaceutical (Contract)
San Rafael, CA
2018 - 2017
● Established an integrated genetic and curated literature workflow to predict incidence and prevalence rates of over sixty rare, genetic disorders, with R statistical and visualization packages (ggplot2) and MATLAB.
● Upgraded and tested RNA-Seq data pipeline (STAR2, SAMtools, Bioconductor) to discern disease contribution of rare variants to neural disease.
● Spearheaded development of three relational databases derived from Hail HPC population genomics platform, in collaboration with software engineer.
● Co-authored manuscript submitted to peer-reviewed publication, on prediction of disease severity in metachromatic leukodystrophy.
● Developed allele-specific association models and GWAS analysis software for two later published manuscripts.
Research Associate
University of Miami Miller School of Medicine, The Miami Project to Cure Paralysis, Pearse Lab
Miami, FL
2017 - 2016
● Mentored research associates in developing bioinformatic skills, specifically in multiple sequence alignment and standard molecular biological protocols (restriction enzyme digestion, gel electrophoresis, spectrophotometry).
● Identified over forty putative conserved vertebrate phosphodiesterase proteins, by using multiple sequence alignment and genomic evidence.
Disclaimer
This resume was made with the R package pagedown and datadrivencv.
Code available on GitHub.
Last updated on 2022-01-25.The most recent version of this resume is available here.
Education
Rowan University, Graduate School of Biomedical Sciences
Master of Biomedical Science (Distinction)
Stratford, NJ
N/A
“Hippocampal long-term potentiation in neurodegenerative disorders”
Prof. Catherine Neary
Florida International University, The Honors College
BSc, Biological Sciences
Miami, FL
Professional Development
Introduction to Genomic Technologies
Johns Hopkins University
Online
2021
Statistics for Genomic Data Science
Johns Hopkins University
Online
2021
Software Carpentry for R and UNIX
University of Miami
Miami, FL
2016
I am an active member of Biostars 
I have participated in several bioinformatics and software workshops and Meetup groups, in both Seattle, WA and San Francisco, CA, including: SF/Bay AI Developers Group, San Jose Data Science and AI/ML Meetup, Hacker Dojo, and Seattle Sequencing
EXTRA-CURRICULAR
San Francisco chapter of Big Gay Frisbee. 2018 - Present.
Seattle Quake gay rugby union. 2016 - 2017.
Publications
Regulating Axonal Responses to Injury: The Intersection between Signaling Pathways Involved in Axon Myelination and The Inhibition of Axon Regeneration.
Frontiers in Molecular Neuroscience. 2016 Jun 8;9:33.
N/A
2016
Rao S.N., Pearse D.D. Manuscript Editor
Conference Papers
Prediction of disease severity in metachromatic leukodystrophy using measures of protein activity and a novel phenotype matrix.
American Society of Human Genetics Virtual Meeting. [Poster] [Forthcoming on bioRxiv.org]
Online
2020
Trinidad M., Hong X., Sacco J., Nguyen H.P., Clark W.T., Froelich S., LeBowitz J.H., Gelb M.H.
Association of HGMD and gnomAD variants of unknown significance with prediction of disease incidence and prevalence.
BioMarin Internal Research and Development Asilomar Conference. [Poster]
Pacific Grove, CA
2018
Sacco J., Clark W.T., Yu K., Wu K., LeBowitz J.H.
Research Projects
Characterization of glycan substrates accumulating in GM1 gangliosidosis
Molecular Genetics and Metabolism Reports. 2019. 21, p.100524. doi:10.1016/j.ymgmr.2019.100524
N/A
2019
Lawrence R., et al.
Teaching
Peer-Led Team Learning (PLTL)
Florida International University
Miami, FL
2009
General Biology II facilitator for two concurrent PLTL courses